Genetic characterization of respiratory syncytial virus highlights a new BA genotype and emergence of the ON1 genotype in Lyon, France, between 2010 and 2014

Abstract : Background Respiratory syncytial virus (RSV) is a well-recognized cause of respiratory tract infections. Based on G gene variations, 11 RSV-A and 36 RSV-B genotypes have been described to date. The ON1 genotype was detected in Ontario in 2010 and subsequently reported in several countries. Objectives The objective of the present study was to investigate for the first time the RSV epidemiology and genotype diversity in France between 2010 and 2014. Study design All respiratory samples received from patients with influenza-like illness or respiratory tract infection were screened for RSV infection by RT-PCR. The results were stratified according to winter season. Among the RSV-positive cases, 117 samples were further investigated for phylogenetic analysis out of 150 randomly selected for sequencing. Results Among the 20,359 cases screened, 14% of the cases were RSV-positive. RSV-A was predominant during the four winter seasons. The first ON1 variant was detected during the 2010–2011 winter and reached 85% of all RSV-A-positive cases in 2013–2014. Most RSV-B was classified as BA9 and BA10 genotypes but a new genotype (BA-Ly) was described. Conclusion As reported in different countries, ON1 variants were firstly detected in 2011 and became the predominant RSV-A genotype in Lyon. Among RSV-B, BA9 was predominant but detected alongside BA10 or a transient genotype (BA-Ly).